6QFS | pdb_00006qfs

Chargeless variant of the Cellulose-binding domain from Cellulomonas fimi

PDB DOI: https://doi.org/10.2210/pdb6QFS/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Cellulomonas fimi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-01-10 Released: 2019-12-18
Deposition Author(s): Young, D.R., Hoejgaard, C., Messens, J., Winther, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.202 (Depositor), 0.205 (DCC)
R-Value Work:
0.177 (Depositor), 0.182 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Charge Interactions in a Highly Charge-depleted Protein

Hervo-Hansen, S., Hojgaard, C., Johansson, K., Wang, Y., Wahni, K., Young, D., Messens, J., Teilum, K., Lindorff-Larsen, K., Winther, J.R.

(2021) J Am Chem Soc

Macromolecule Content

Total Structure Weight: 90.43 kDa
Atom Count: 6,683
Modeled Residue Count: 841
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exoglucanase/xylanase	A, B, C, D, E A, B, C, D, E, F, G, H	106	Cellulomonas fimi	Mutation(s): 0 Gene Names: cex, xynB EC: 3.2.1.91 (PDB Primary Data), 3.2.1.8 (PDB Primary Data)
UniProt
Find proteins for P07986 (Cellulomonas fimi) Explore P07986 Go to UniProtKB: P07986
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07986
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ETE Query on ETE Download:Ideal Coordinates CCD File SDF format, chain UA [auth E] SDF format, chain NA [auth D] MOL2 format, chain UA [auth E] MOL2 format, chain NA [auth D] mmCIF format, chain UA [auth E] mmCIF format, chain NA [auth D]	NA [auth D], UA [auth E]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₉ H₂₀ O₅ ZNYRFEPBTVGZDN-UHFFFAOYSA-N		Interactions Focus chain NA [auth D] Focus chain UA [auth E] Interactions & Density Focus chain NA [auth D] Focus chain UA [auth E]
1PS Query on 1PS Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain M [auth B] SDF format, chain OA [auth E] SDF format, chain VA [auth F] MOL2 format, chain FA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain OA [auth E] MOL2 format, chain VA [auth F] mmCIF format, chain FA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain OA [auth E] mmCIF format, chain VA [auth F]	FA [auth D], M [auth B], OA [auth E], VA [auth F]	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE C₈ H₁₁ N O₃ S REEBJQTUIJTGAL-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain M [auth B] Focus chain OA [auth E] Focus chain VA [auth F] Interactions & Density Focus chain FA [auth D] Focus chain M [auth B] Focus chain OA [auth E] Focus chain VA [auth F]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain MA [auth D] SDF format, chain NB [auth H] MOL2 format, chain MA [auth D] MOL2 format, chain NB [auth H] mmCIF format, chain MA [auth D] mmCIF format, chain NB [auth H]	MA [auth D], NB [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain MA [auth D] Focus chain NB [auth H] Interactions & Density Focus chain MA [auth D] Focus chain NB [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CB [auth F] MOL2 format, chain CB [auth F] mmCIF format, chain CB [auth F]	CB [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CB [auth F] Interactions & Density Focus chain CB [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EB [auth G] SDF format, chain FB [auth G] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain WA [auth F] SDF format, chain P [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain FB [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain P [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain FB [auth G] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain WA [auth F] mmCIF format, chain P [auth B]	AA [auth C] EB [auth G] FB [auth G] HA [auth D] IA [auth D] AA [auth C], EB [auth G], FB [auth G], HA [auth D], IA [auth D], J [auth A], N [auth B], O [auth B], P [auth B], PA [auth E], QA [auth E], W [auth C], WA [auth F], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain W [auth C] Focus chain WA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain W [auth C] Focus chain WA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain I [auth A] SDF format, chain KB [auth H] SDF format, chain S [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain T [auth C] SDF format, chain DB [auth G] MOL2 format, chain GA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain KB [auth H] MOL2 format, chain S [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain T [auth C] MOL2 format, chain DB [auth G] mmCIF format, chain GA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain KB [auth H] mmCIF format, chain S [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain T [auth C] mmCIF format, chain DB [auth G]	DB [auth G] GA [auth D] I [auth A] KB [auth H] S [auth C] DB [auth G], GA [auth D], I [auth A], KB [auth H], S [auth C], T [auth C], U [auth C], V [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DB [auth G] Focus chain GA [auth D] Focus chain I [auth A] Focus chain KB [auth H] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain DB [auth G] Focus chain GA [auth D] Focus chain I [auth A] Focus chain KB [auth H] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain GB [auth G] SDF format, chain HB [auth G] SDF format, chain IB [auth G] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain LB [auth H] SDF format, chain MB [auth H] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain SA [auth E] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] SDF format, chain XA [auth F] SDF format, chain TA [auth E] SDF format, chain L [auth A] SDF format, chain JB [auth G] SDF format, chain EA [auth C] SDF format, chain BA [auth C] SDF format, chain AB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain HB [auth G] MOL2 format, chain IB [auth G] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth H] MOL2 format, chain MB [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain TA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain JB [auth G] MOL2 format, chain EA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth F] mmCIF format, chain BB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain GB [auth G] mmCIF format, chain HB [auth G] mmCIF format, chain IB [auth G] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth H] mmCIF format, chain MB [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain SA [auth E] mmCIF format, chain YA [auth F] mmCIF format, chain ZA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain TA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain JB [auth G] mmCIF format, chain EA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth F]	AB [auth F] BA [auth C] BB [auth F] CA [auth C] DA [auth C] AB [auth F], BA [auth C], BB [auth F], CA [auth C], DA [auth C], EA [auth C], GB [auth G], HB [auth G], IB [auth G], JA [auth D], JB [auth G], K [auth A], KA [auth D], L [auth A], LA [auth D], LB [auth H], MB [auth H], Q [auth B], R [auth B], RA [auth E], SA [auth E], TA [auth E], XA [auth F], YA [auth F], ZA [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain MB [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain MB [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain ZA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.202 (Depositor), 0.205 (DCC)
R-Value Work: 0.177 (Depositor), 0.182 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.382	α = 90
b = 137.382	β = 90
c = 148.548	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
	Belgium	--

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 1.1: 2021-01-27
Changes: Database references, Structure summary
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary